-
1
-
-
85020080492
-
Deblur rapidly resolves single-nucleotide community sequence patterns
-
Amir A, McDonald D, Navas-Molina JA, Kopylova E, Morton JT, Xu ZZ et al. (2017). Deblur rapidly resolves single-nucleotide community sequence patterns. mSystems 2: e00191-16.
-
(2017)
MSystems
, vol.2
, pp. e00191-e00216
-
-
Amir, A.1
McDonald, D.2
Navas-Molina, J.A.3
Kopylova, E.4
Morton, J.T.5
Xu, Z.Z.6
-
2
-
-
84963525850
-
Microbiota-based model improves the sensitivity of fecal immunochemical test for detecting colonic lesions
-
Baxter NT, Ruffin MT, Rogers MA, Schloss PD. (2016). Microbiota-based model improves the sensitivity of fecal immunochemical test for detecting colonic lesions. Genome Med 8: 37.
-
(2016)
Genome Med
, vol.8
, pp. 37
-
-
Baxter, N.T.1
Ruffin, M.T.2
Rogers, M.A.3
Schloss, P.D.4
-
3
-
-
85016628377
-
Are oligotypes meaningful ecological and phylogenetic units? A case study of Microcystis in freshwater lakes
-
Berry MA, White JD, Davis TW, Jain S, Johengen TH, Dick GJ et al. (2017). Are oligotypes meaningful ecological and phylogenetic units? A case study of Microcystis in freshwater lakes. Front Microbiol 8: 365.
-
(2017)
Front Microbiol
, vol.8
, pp. 365
-
-
Berry, M.A.1
White, J.D.2
Davis, T.W.3
Jain, S.4
Johengen, T.H.5
Dick, G.J.6
-
4
-
-
84871979584
-
Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing
-
Bokulich NA, Subramanian S, Faith JJ, Gevers D, Gordon JI, Knight R et al. (2013). Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing. Nat Methods 10: 57-59.
-
(2013)
Nat Methods
, vol.10
, pp. 57-59
-
-
Bokulich, N.A.1
Subramanian, S.2
Faith, J.J.3
Gevers, D.4
Gordon, J.I.5
Knight, R.6
-
5
-
-
84969871954
-
DADA2: High-resolution sample inference from Illumina amplicon data
-
Callahan BJ, McMurdie PJ, Rosen MJ, Han AW, Johnson AJ, Holmes SP. (2016a). DADA2: high-resolution sample inference from Illumina amplicon data. Nat Methods 13: 581-583.
-
(2016)
Nat Methods
, vol.13
, pp. 581-583
-
-
Callahan, B.J.1
McMurdie, P.J.2
Rosen, M.J.3
Han, A.W.4
Johnson, A.J.5
Holmes, S.P.6
-
6
-
-
85010953137
-
Bioconductor workflow for microbiome data analysis: From raw reads to community analyses
-
Callahan BJ, Sankaran K, Fukuyama JA, McMurdie PJ, Holmes SP. (2016b). Bioconductor workflow for microbiome data analysis: from raw reads to community analyses. F1000Res 5: 1492.
-
(2016)
F1000Res
, vol.5
, pp. 1492
-
-
Callahan, B.J.1
Sankaran, K.2
Fukuyama, J.A.3
McMurdie, P.J.4
Holmes, S.P.5
-
7
-
-
84929996994
-
Eukaryotic plankton diversity in the sunlit ocean
-
De Vargas C, Audic S, Henry N, Decelle J, Mahé F, Logares R et al. (2015). Eukaryotic plankton diversity in the sunlit ocean. Science 348: 1261605.
-
(2015)
Science
, vol.348
, pp. 1261605
-
-
De Vargas, C.1
Audic, S.2
Henry, N.3
Decelle, J.4
Mahé, F.5
Logares, R.6
-
8
-
-
84941005620
-
Temporal and spatial variation of the human microbiota during pregnancy
-
DiGiulio DB, Callahan BJ, McMurdie PJ, Costello EK, Lyell DJ, Robaczewska A et al. (2015). Temporal and spatial variation of the human microbiota during pregnancy. Proc Natl Acad Sci USA 112: 11060-11065.
-
(2015)
Proc Natl Acad Sci USA
, vol.112
, pp. 11060-11065
-
-
DiGiulio, D.B.1
Callahan, B.J.2
McMurdie, P.J.3
Costello, E.K.4
Lyell, D.J.5
Robaczewska, A.6
-
9
-
-
84947549603
-
Error filtering, pair assembly and error correction for next-generation sequencing reads
-
Edgar RC, Flyvbjerg H. (2015). Error filtering, pair assembly and error correction for next-generation sequencing reads. Bioinformatics 31: 3476-3482.
-
(2015)
Bioinformatics
, vol.31
, pp. 3476-3482
-
-
Edgar, R.C.1
Flyvbjerg, H.2
-
11
-
-
84889649570
-
Oligotyping: Differentiating between closely related microbial taxa using 16 S rRNA gene data
-
Eren AM, Maignien L, Sul WJ, Murphy LG, Grim SL, Morrison HG et al. (2013). Oligotyping: differentiating between closely related microbial taxa using 16 S rRNA gene data. Methods Ecol Evol 4: 1111-1119.
-
(2013)
Methods Ecol Evol
, vol.4
, pp. 1111-1119
-
-
Eren, A.M.1
Maignien, L.2
Sul, W.J.3
Murphy, L.G.4
Grim, S.L.5
Morrison, H.G.6
-
12
-
-
84925044505
-
Minimum entropy decomposition: Unsupervised oligotyping for sensitive partitioning of high-throughput marker gene sequences
-
Eren AM, Morrison HG, Lescault PJ, Reveillaud J, Vineis JH, Sogin ML. (2015). Minimum entropy decomposition: unsupervised oligotyping for sensitive partitioning of high-throughput marker gene sequences. ISME J 9: 968-979.
-
(2015)
ISME J
, vol.9
, pp. 968-979
-
-
Eren, A.M.1
Morrison, H.G.2
Lescault, P.J.3
Reveillaud, J.4
Vineis, J.H.5
Sogin, M.L.6
-
13
-
-
84989162248
-
Editorial: New insights into microbial ecology through subtle nucleotide variation
-
Eren AM, Sogin ML, Maignien L. (2016). Editorial: New insights into microbial ecology through subtle nucleotide variation. Front Microbiol 7: 1318.
-
(2016)
Front Microbiol
, vol.7
, pp. 1318
-
-
Eren, A.M.1
Sogin, M.L.2
Maignien, L.3
-
14
-
-
85041918285
-
Open-source sequence clustering methods improve the state of the art
-
Kopylova E, Navas-Molina JA, Mercier C, Xu ZZ, Mahé F, He Y et al. (2016). Open-source sequence clustering methods improve the state of the art. mSystems 1: e00003-e00015.
-
(2016)
MSystems
, vol.1
, pp. e00003-e00015
-
-
Kopylova, E.1
Navas-Molina, J.A.2
Mercier, C.3
Xu, Z.Z.4
Mahé, F.5
He, Y.6
-
15
-
-
84884251320
-
Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform
-
Kozich JJ, Westcott SL, Baxter NT, Highlander SK, Schloss PD. (2013). Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform. Appl Environ Microbiol 79: 5112-5120.
-
(2013)
Appl Environ Microbiol
, vol.79
, pp. 5112-5120
-
-
Kozich, J.J.1
Westcott, S.L.2
Baxter, N.T.3
Highlander, S.K.4
Schloss, P.D.5
-
16
-
-
84951008522
-
Swarm v2: Highly-scalable and high-resolution amplicon clustering
-
Mahé F, Rognes T, Quince C, De Vargas C, Dunthorn M. (2015). Swarm v2: highly-scalable and high-resolution amplicon clustering. PeerJ 3: e1420.
-
(2015)
PeerJ
, vol.3
, pp. e1420
-
-
Mahé, F.1
Rognes, T.2
Quince, C.3
De Vargas, C.4
Dunthorn, M.5
-
17
-
-
85017450301
-
Ecological dynamics and co-occurrence among marine phytoplankton, bacteria and myoviruses shows microdiversity matters
-
Needham DM, Sachdeva R, Fuhrman JA. (2017). Ecological dynamics and co-occurrence among marine phytoplankton, bacteria and myoviruses shows microdiversity matters. ISME J 11 (7): 1614-1629.
-
(2017)
ISME J
, vol.11
, Issue.7
, pp. 1614-1629
-
-
Needham, D.M.1
Sachdeva, R.2
Fuhrman, J.A.3
-
18
-
-
84920714710
-
Subsampled openreference clustering creates consistent, comprehensive OTU definitions and scales to billions of sequences
-
Rideout JR, He Y, Navas-Molina JA, Walters WA, Ursell LK, Gibbons SM et al. (2014). Subsampled openreference clustering creates consistent, comprehensive OTU definitions and scales to billions of sequences. PeerJ 2: e545.
-
(2014)
PeerJ
, vol.2
, pp. e545
-
-
Rideout, J.R.1
He, Y.2
Navas-Molina, J.A.3
Walters, W.A.4
Ursell, L.K.5
Gibbons, S.M.6
-
19
-
-
33947302827
-
Taxonomic parameters revisited: Tarnished gold standards
-
Stackebrandt E, Ebers J. (2006). Taxonomic parameters revisited: tarnished gold standards. Microbiology Today 33: 152.
-
(2006)
Microbiology Today
, vol.33
, pp. 152
-
-
Stackebrandt, E.1
Ebers, J.2
-
20
-
-
84923545661
-
Interpreting 16 S metagenomic data without clustering to achieve sub-OTU resolution
-
Tikhonov M, Leach RW, Wingreen NS. (2015). Interpreting 16 S metagenomic data without clustering to achieve sub-OTU resolution. ISME J 9: 68-80.
-
(2015)
ISME J
, vol.9
, pp. 68-80
-
-
Tikhonov, M.1
Leach, R.W.2
Wingreen, N.S.3
-
22
-
-
84951059585
-
De novo clustering methods outperform reference-based methods for assigning 16 S rRNA gene sequences to operational taxonomic units
-
Westcott SL, Schloss PD. (2015). De novo clustering methods outperform reference-based methods for assigning 16 S rRNA gene sequences to operational taxonomic units. PeerJ 3: e1487.
-
(2015)
PeerJ
, vol.3
, pp. e1487
-
-
Westcott, S.L.1
Schloss, P.D.2
|